EDIT

// $Id$

/**

 * Copyright (C) 2007 EDIT

 * European Distributed Institute of Taxonomy 

 * http://www.e-taxonomy.eu

 * 

 * The contents of this file are subject to the Mozilla Public License Version 1.1

 * See LICENSE.TXT at the top of this package for the full license terms.

 */

package eu.etaxonomy.cdm.model.description;

import java.io.PrintStream;

import java.util.HashSet;

import java.util.Set;

import javax.persistence.Entity;

import javax.persistence.FetchType;

import javax.persistence.JoinColumn;

import javax.persistence.JoinTable;

import javax.persistence.ManyToMany;

import javax.persistence.OneToOne;

import javax.validation.constraints.NotNull;

import javax.xml.bind.annotation.XmlAccessType;

import javax.xml.bind.annotation.XmlAccessorType;

import javax.xml.bind.annotation.XmlElement;

import javax.xml.bind.annotation.XmlElementWrapper;

import javax.xml.bind.annotation.XmlIDREF;

import javax.xml.bind.annotation.XmlRootElement;

import javax.xml.bind.annotation.XmlSchemaType;

import javax.xml.bind.annotation.XmlType;

import org.apache.log4j.Logger;

import org.hibernate.annotations.Cascade;

import org.hibernate.annotations.CascadeType;

import org.hibernate.envers.Audited;

import org.hibernate.search.annotations.Indexed;

import org.hibernate.tool.hbm2x.StringUtils;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.model.common.IdentifiableEntity;

import eu.etaxonomy.cdm.model.common.Language;

import eu.etaxonomy.cdm.model.location.NamedArea;

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.strategy.generate.PolytomousKeyGenerator;

/**

 * The class allowing the representation of single-access fixed dichotomous or

 * polytomous decision keys used to identify {@link SpecimenOrObservationBase

 * specimens or observations} (this means to assign {@link Taxon taxa} to). The

 * key may be written by an author or may be generated by the

 * {@link PolytomousKeyGenerator}. The different paths to the taxa are expressed

 * by a decision graph consisting of {@link PolytomousKeyNode

 * PolytomousKeyNodes}. The root node of such graph is accessible by

 * {@link #getRoot()}. Please refer to {@link PolytomousKeyNode} for detailed

 * documentation on this decision graph please

 * 

 * @author h.fradin

 * @created 13.08.2009

 * @version 1.0

 * 

 * @author a.mueller

 * @created 08.11.2010

 * @version 2.0

 */

@XmlAccessorType(XmlAccessType.FIELD)

@XmlType(name = "PolytomousKey", propOrder = { "coveredTaxa", "taxonomicScope",

		"geographicalScope", "scopeRestrictions", "root" })

@XmlRootElement(name = "PolytomousKey")

@Entity

@Indexed(index = "eu.etaxonomy.cdm.model.media.FeatureTree")

@Audited

public class PolytomousKey extends IdentifiableEntity implements IIdentificationKey {

	private static final long serialVersionUID = -3368243754557343942L;

	private static final Logger logger = Logger.getLogger(PolytomousKey.class);

	@XmlElementWrapper(name = "CoveredTaxa")

	@XmlElement(name = "CoveredTaxon")

	@XmlIDREF

	@XmlSchemaType(name = "IDREF")

	@ManyToMany(fetch = FetchType.LAZY)

	@NotNull

	@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})

	private Set<Taxon> coveredTaxa = new HashSet<Taxon>();

	@XmlElementWrapper(name = "TaxonomicScope")

	@XmlElement(name = "Taxon")

	@XmlIDREF

	@XmlSchemaType(name = "IDREF")

	@ManyToMany(fetch = FetchType.LAZY)

	@JoinTable(name = "PolytomousKey_Taxon", joinColumns = @JoinColumn(name = "polytomousKey_id"), inverseJoinColumns = @JoinColumn(name = "taxon_id"))

	@NotNull

	@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})

	private Set<Taxon> taxonomicScope = new HashSet<Taxon>();

	@XmlElementWrapper(name = "GeographicalScope")

	@XmlElement(name = "Area")

	@XmlIDREF

	@XmlSchemaType(name = "IDREF")

	@ManyToMany(fetch = FetchType.LAZY)

	@JoinTable(name = "PolytomousKey_NamedArea")

	@NotNull

	private Set<NamedArea> geographicalScope = new HashSet<NamedArea>();

	@XmlElementWrapper(name = "ScopeRestrictions")

	@XmlElement(name = "Restriction")

	@XmlIDREF

	@XmlSchemaType(name = "IDREF")

	@ManyToMany(fetch = FetchType.LAZY)

	@JoinTable(name = "PolytomousKey_Scope")

	@NotNull

	private Set<Scope> scopeRestrictions = new HashSet<Scope>();

	@XmlElement(name = "Root")

	@OneToOne(fetch = FetchType.LAZY)

	@Cascade({ CascadeType.SAVE_UPDATE, CascadeType.MERGE })

	private PolytomousKeyNode root;

	// ******************************** STATIC METHODS

	// ********************************/

	/**

	 * Creates a new empty identification multi-access key instance.

	 */

	public static PolytomousKey NewInstance() {

		return new PolytomousKey();

	}

	/**

	 * Creates a new empty identification polytomous key instance.

	 */

	public static PolytomousKey NewTitledInstance(String title) {

		PolytomousKey result = new PolytomousKey();

		result.setTitleCache(title, true);

		return result;

	}

	// ************************** CONSTRUCTOR

	// *******************************************/

	/**

	 * Class constructor: creates a new empty multi-access key instance.

	 */

	protected PolytomousKey() {

		super();

		root = PolytomousKeyNode.NewRootInstance();

		root.setKey(this);

	}

	// ************************ GETTER/ SETTER

	/**

	 * Returns the topmost {@link PolytomousKeyNode polytomous key node} (root

	 * node) of <i>this</i> polytomous key. The root node does not have any

	 * parent. Since polytomous key nodes recursively point to their child nodes

	 * the complete polytomous key is defined by its root node.

	 */

	public PolytomousKeyNode getRoot() {

		return root;

	}

	/**

	 * This method should be used by Hibernate only. If we want to make this

	 * method public we have to think about biderionality and also what should

	 * happen with the old root node.

	 * 

	 * @see #getRoot()

	 */

	public void setRoot(PolytomousKeyNode root) {

		this.root = root;

	}

	/**

	 * Returns the set of possible {@link Taxon taxa} corresponding to

	 * <i>this</i> identification key.

	 */

	public Set<Taxon> getCoveredTaxa() {

		if (coveredTaxa == null) {

			this.coveredTaxa = new HashSet<Taxon>();

		}

		return coveredTaxa;

	}

	/**

	 * @see #getCoveredTaxa()

	 */

	protected void setCoveredTaxa(Set<Taxon> coveredTaxa) {

		this.coveredTaxa = coveredTaxa;

	}

	/**

	 * Adds a {@link Taxon taxa} to the set of {@link #getCoveredTaxa() covered

	 * taxa} corresponding to <i>this</i> identification key.

	 * 

	 * @param taxon

	 *            the taxon to be added to <i>this</i> identification key

	 * @see #getCoveredTaxa()

	 */

	public void addCoveredTaxon(Taxon taxon) {

		this.coveredTaxa.add(taxon);

	}

	/**

	 * Removes one element from the set of {@link #getCoveredTaxa() covered

	 * taxa} corresponding to <i>this</i> identification key.

	 * 

	 * @param taxon

	 *            the taxon which should be removed

	 * @see #getCoveredTaxa()

	 * @see #addCoveredTaxon(Taxon)

	 */

	public void removeCoveredTaxon(Taxon taxon) {

		this.coveredTaxa.remove(taxon);

	}

	/**

	 * Returns the set of {@link NamedArea named areas} indicating the

	 * geospatial data where <i>this</i> identification key is valid.

	 */

	public Set<NamedArea> getGeographicalScope() {

		if (geographicalScope == null) {

			this.geographicalScope = new HashSet<NamedArea>();

		}

		return geographicalScope;

	}

	/**

	 * Adds a {@link NamedArea geoScope} to the set of {@link #getGeoScopes()

	 * geogspatial scopes} corresponding to <i>this</i> identification key.

	 * 

	 * @param geoScope

	 *            the named area to be added to <i>this</i> identification key

	 * @see #getGeoScopes()

	 */

	public void addGeographicalScope(NamedArea geoScope) {

		this.geographicalScope.add(geoScope);

	}

	/**

	 * Removes one element from the set of {@link #getGeoScopes() geogspatial

	 * scopes} corresponding to <i>this</i> identification key.

	 * 

	 * @param geoScope

	 *            the named area which should be removed

	 * @see #getGeoScopes()

	 * @see #addGeoScope(NamedArea)

	 */

	public void removeGeographicalScope(NamedArea geoScope) {

		this.geographicalScope.remove(geoScope);

	}

	/**

	 * Returns the set of {@link Taxon taxa} that define the taxonomic scope of

	 * <i>this</i> identification key

	 */

	public Set<Taxon> getTaxonomicScope() {

		if (taxonomicScope == null) {

			this.taxonomicScope = new HashSet<Taxon>();

		}

		return taxonomicScope;

	}

	/**

	 * Adds a {@link Taxon taxa} to the set of {@link #getTaxonomicScope()

	 * taxonomic scopes} corresponding to <i>this</i> identification key.

	 * 

	 * @param taxon

	 *            the taxon to be added to <i>this</i> identification key

	 * @see #getTaxonomicScope()

	 */

	public void addTaxonomicScope(Taxon taxon) {

		this.taxonomicScope.add(taxon);

	}

	/**

	 * Removes one element from the set of {@link #getTaxonomicScope() taxonomic

	 * scopes} corresponding to <i>this</i> identification key.

	 * 

	 * @param taxon

	 *            the taxon which should be removed

	 * @see #getTaxonomicScope()

	 * @see #addTaxonomicScope(Taxon)

	 */

	public void removeTaxonomicScope(Taxon taxon) {

		this.taxonomicScope.remove(taxon);

	}

	/**

	 * Returns the set of {@link Scope scope restrictions} corresponding to

	 * <i>this</i> identification key

	 */

	public Set<Scope> getScopeRestrictions() {

		if (scopeRestrictions == null) {

			this.scopeRestrictions = new HashSet<Scope>();

		}

		return scopeRestrictions;

	}

	/**

	 * Adds a {@link Scope scope restriction} to the set of

	 * {@link #getScopeRestrictions() scope restrictions} corresponding to

	 * <i>this</i> identification key.

	 * 

	 * @param scopeRestriction

	 *            the scope restriction to be added to <i>this</i>

	 *            identification key

	 * @see #getScopeRestrictions()

	 */

	public void addScopeRestriction(Scope scopeRestriction) {

		this.scopeRestrictions.add(scopeRestriction);

	}

	/**

	 * Removes one element from the set of {@link #getScopeRestrictions() scope

	 * restrictions} corresponding to <i>this</i> identification key.

	 * 

	 * @param scopeRestriction

	 *            the scope restriction which should be removed

	 * @see #getScopeRestrictions()

	 * @see #addScopeRestriction(Scope)

	 */

	public void removeScopeRestriction(Scope scopeRestriction) {

		this.scopeRestrictions.remove(scopeRestriction);

	}

	// ******************** toString *****************************************/

	private class IntegerObject {

		int number = 0;

		int inc() {

			return number++;

		};

		@Override

		public String toString() {

			return String.valueOf(number);

		}

	}

	public String print(PrintStream stream) {

		String title = this.getTitleCache() + "\n";

		String strPrint = title;

		if (stream != null) {

			stream.print(title);

		}

		PolytomousKeyNode root = this.getRoot();

		strPrint += printNode(root, null, "  ", stream);

		return strPrint;

	}

	/**

	 * TODO this is a preliminary implementation

	 * 

	 * @param node

	 * @param identation

	 * @param no

	 * @param myNumber

	 * @param stream

	 * @return

	 */

	private String printNode(PolytomousKeyNode node, PolytomousKeyNode parent2,

			String identation, PrintStream stream) {

		String separator = ", ";

		String result = identation + node.getNodeNumber() + ". ";

		if (node != null) {

			// key choice

			String question = null;

			String feature = null;

			if (node.getQuestion() != null) {

				question = node.getQuestion().getLabelText(Language.DEFAULT());

			}

			if (node.getFeature() != null) {

				feature = node.getFeature().getLabel(Language.DEFAULT());

			}

			result += CdmUtils.concat(" - ", question, feature) + "\n";

			;

			// Leads

			char nextCounter = 'a';

			for (PolytomousKeyNode child : node.getChildren()) {

				String leadNumber = String.valueOf(nextCounter++);

				if (child.getStatement() != null) {

					String statement = child.getStatement().getLabelText(

							Language.DEFAULT());

					result += identation + "  " + leadNumber + ") "

							+ (statement == null ? "" : (statement));

					result += " ... ";

					// child node

					if (!child.isLeaf()) {

						result += child.getNodeNumber() + separator;

					}

					// taxon

					if (child.getTaxon() != null) {

						String strTaxon = "";

						if (child.getTaxon().getName() != null) {

							strTaxon = child.getTaxon().getName()

									.getTitleCache();

						} else {

							strTaxon = child.getTaxon().getTitleCache();

						}

						result += strTaxon + separator;

					}

					// subkey

					if (child.getSubkey() != null) {

						String subkey = child.getSubkey().getTitleCache();

						result += subkey + separator;

					}

					// other node

					if (child.getOtherNode() != null) {

						PolytomousKeyNode otherNode = child.getOtherNode();

						String otherNodeString = null;

						if (child.getKey().equals(otherNode.getKey())) {

							otherNodeString = String.valueOf(otherNode

									.getNodeNumber());

						} else {

							otherNodeString = otherNode.getKey() + " "

									+ otherNode.getNodeNumber();

						}

						result += otherNodeString + separator;

					}

					result = StringUtils.chompLast(result, separator);

					result += "\n";

				}

			}

			if (stream != null) {

				stream.print(result);

			}

			for (PolytomousKeyNode child : node.getChildren()) {

				if (!child.isLeaf()) {

					result += printNode(child, node, identation + "", stream);

				}

			}

		}

		return result;

	}

	//

	// public List<PolytomousKeyNode> getChildren() {

	// return getRoot().getChildren();

	// }

	// *********************** CLONE

	// ********************************************************/

	/**

	 * Clones <i>this</i> PolytomousKey. This is a shortcut that enables to

	 * create a new instance that differs only slightly from <i>this</i>

	 * PolytomousKey by modifying only some of the attributes.

	 * 

	 * @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#clone()

	 * @see java.lang.Object#clone()

	 */

	@Override

	public Object clone() {

		PolytomousKey result;

		try {

			result = (PolytomousKey) super.clone();

			result.coveredTaxa = new HashSet<Taxon>();

			for (Taxon taxon : this.coveredTaxa) {

				result.addCoveredTaxon(taxon);

			}

			result.geographicalScope = new HashSet<NamedArea>();

			for (NamedArea area : this.geographicalScope) {

				result.addGeographicalScope(area);

			}

			result.root = (PolytomousKeyNode) this.root.clone();

			result.scopeRestrictions = new HashSet<Scope>();

			for (Scope scope : this.scopeRestrictions) {

				result.addScopeRestriction(scope);

			}

			result.taxonomicScope = new HashSet<Taxon>();

			for (Taxon taxon : this.taxonomicScope) {

				result.addTaxonomicScope(taxon);

			}

			return result;

		} catch (CloneNotSupportedException e) {

			logger.warn("Object does not implement cloneable");

			e.printStackTrace();

			return null;

		}

	}

}